I have a world I have played since 1.14 that has several locations built up but large portions of the nether were left unexplored to allow new biomes to appear this has worked. So I set about connecting areas via nether portals. At least two locations that had player built structures and chests, have been reset and now contain nothing, one of which was the location of the worlds stronghold. I have past backups that were made before 1.16, and reloading these I can verify these locations still exist. One happened as I went through an existing nether portal that existed in the part of the nether I had built in, this was after travelling back there via the nether to make a safe route between 2 points on the nether. I reloaded a backup and travelled there via the overworld holding a map with said buildings on, as soon as i entered the chunk the map reset and everything was lost. The second time was on returning to the stronghold area and finding everything gone, again confirmed via reloading backups, however this time entering the area on the backups does not reset it, so its not entirely down to 1.16 running a 1.14 made map. 

Is there anyway to copy individual chunks from one save file into another? I had done alot of work on this world and am now nervous to continue playing as I don't know when a new chunk will reset over another its happened twice in 1 week.  My most used areas seem to however be fine. 

The two pictures are the exact same location, from a backup and the current save. I  have played Minecraft Bedrock since I switched over from Java when Win 10 edition was given away, never witnessed this before on any of the other worlds and they all went through version changes, I started again because I couldnt find bees in any of my prior worlds.